Starting phenix.real_space_refine on Sun Jul 5 11:45:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wte_32780/07_2026/7wte_32780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wte_32780/07_2026/7wte_32780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wte_32780/07_2026/7wte_32780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wte_32780/07_2026/7wte_32780.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wte_32780/07_2026/7wte_32780.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wte_32780/07_2026/7wte_32780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wte_32780/07_2026/7wte_32780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wte_32780/07_2026/7wte_32780.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 152 5.16 5 C 17172 2.51 5 N 4735 2.21 5 O 5089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27160 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4625 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 40, 'TRANS': 559} Chain: "B" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4625 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 40, 'TRANS': 559} Chain: "C" Number of atoms: 8869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8869 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 65, 'TRANS': 1080} Chain: "D" Number of atoms: 8877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8877 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 65, 'TRANS': 1081} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'ACO': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'ACO': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.54, per 1000 atoms: 0.20 Number of scatterers: 27160 At special positions: 0 Unit cell: (161.7, 160.6, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 12 15.00 O 5089 8.00 N 4735 7.00 C 17172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 786 " distance=2.03 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.02 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 786 " distance=2.02 Simple disulfide: pdb=" SG CYS D 752 " - pdb=" SG CYS D 786 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6430 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 24 sheets defined 47.8% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 540 through 549 removed outlier: 4.032A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 583 through 598 removed outlier: 3.852A pdb=" N LEU A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 608 through 613 removed outlier: 4.277A pdb=" N PHE A 612 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASP A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 613' Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 622 through 634 removed outlier: 3.975A pdb=" N GLU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 removed outlier: 3.674A pdb=" N VAL A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 removed outlier: 3.605A pdb=" N MET A 686 " --> pdb=" O TYR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 734 Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'A' and resid 778 through 788 Processing helix chain 'A' and resid 809 through 817 removed outlier: 3.552A pdb=" N LEU A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 843 removed outlier: 3.936A pdb=" N VAL A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 removed outlier: 4.205A pdb=" N THR A 853 " --> pdb=" O ASP A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 867 through 882 Processing helix chain 'A' and resid 883 through 886 Processing helix chain 'A' and resid 887 through 901 removed outlier: 3.955A pdb=" N VAL A 895 " --> pdb=" O LYS A 891 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 924 Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 941 through 949 Processing helix chain 'A' and resid 960 through 969 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.968A pdb=" N SER A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.733A pdb=" N LEU A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1013 through 1028 Processing helix chain 'A' and resid 1034 through 1040 Processing helix chain 'B' and resid 496 through 510 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 571 through 578 removed outlier: 4.200A pdb=" N GLN B 575 " --> pdb=" O ARG B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 590 through 598 removed outlier: 3.701A pdb=" N HIS B 596 " --> pdb=" O PRO B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 612 removed outlier: 3.787A pdb=" N THR B 611 " --> pdb=" O GLY B 608 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 612 " --> pdb=" O GLY B 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 608 through 612' Processing helix chain 'B' and resid 613 through 618 Processing helix chain 'B' and resid 622 through 631 removed outlier: 3.533A pdb=" N GLU B 629 " --> pdb=" O ARG B 625 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B 630 " --> pdb=" O ARG B 626 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 removed outlier: 3.554A pdb=" N VAL B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 697 removed outlier: 3.571A pdb=" N MET B 686 " --> pdb=" O TYR B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 734 removed outlier: 3.823A pdb=" N TYR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 removed outlier: 3.526A pdb=" N ARG B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 790 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 809 through 817 removed outlier: 3.862A pdb=" N LEU B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 843 removed outlier: 4.049A pdb=" N VAL B 831 " --> pdb=" O PRO B 827 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 846 No H-bonds generated for 'chain 'B' and resid 844 through 846' Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 867 through 881 removed outlier: 3.845A pdb=" N ASN B 873 " --> pdb=" O GLY B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 902 removed outlier: 3.781A pdb=" N GLU B 889 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 925 Processing helix chain 'B' and resid 927 through 934 Processing helix chain 'B' and resid 941 through 950 Processing helix chain 'B' and resid 960 through 969 removed outlier: 3.797A pdb=" N ARG B 964 " --> pdb=" O PRO B 960 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 969 " --> pdb=" O SER B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 987 through 998 removed outlier: 3.524A pdb=" N GLU B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1013 Processing helix chain 'B' and resid 1013 through 1028 Processing helix chain 'B' and resid 1034 through 1040 Processing helix chain 'C' and resid 46 through 59 removed outlier: 3.663A pdb=" N ILE C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 109 removed outlier: 3.548A pdb=" N ASN C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.675A pdb=" N ALA C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 149 Processing helix chain 'C' and resid 151 through 162 removed outlier: 3.847A pdb=" N ALA C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.547A pdb=" N TYR C 187 " --> pdb=" O PHE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 227 removed outlier: 3.759A pdb=" N GLU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 303 Processing helix chain 'C' and resid 332 through 341 removed outlier: 4.516A pdb=" N THR C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 354 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 435 through 450 Processing helix chain 'C' and resid 458 through 468 removed outlier: 3.621A pdb=" N LEU C 462 " --> pdb=" O ASN C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 474 removed outlier: 3.517A pdb=" N GLY C 474 " --> pdb=" O GLN C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 481 removed outlier: 4.384A pdb=" N ILE C 481 " --> pdb=" O THR C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.663A pdb=" N LEU C 500 " --> pdb=" O ARG C 496 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 571 through 578 removed outlier: 4.208A pdb=" N GLN C 575 " --> pdb=" O ARG C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 589 removed outlier: 3.838A pdb=" N LYS C 589 " --> pdb=" O ASP C 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 586 through 589' Processing helix chain 'C' and resid 590 through 598 removed outlier: 3.700A pdb=" N HIS C 596 " --> pdb=" O PRO C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.739A pdb=" N THR C 611 " --> pdb=" O GLY C 608 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE C 612 " --> pdb=" O GLY C 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 622 through 634 removed outlier: 4.417A pdb=" N GLU C 629 " --> pdb=" O ARG C 625 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 630 " --> pdb=" O ARG C 626 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU C 632 " --> pdb=" O GLN C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 removed outlier: 3.658A pdb=" N GLY C 670 " --> pdb=" O ALA C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 697 removed outlier: 3.688A pdb=" N MET C 686 " --> pdb=" O TYR C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 734 removed outlier: 3.593A pdb=" N TYR C 723 " --> pdb=" O SER C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 removed outlier: 4.327A pdb=" N ARG C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 790 Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.504A pdb=" N SER C 802 " --> pdb=" O ASP C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 817 removed outlier: 3.802A pdb=" N LEU C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 843 removed outlier: 4.198A pdb=" N VAL C 831 " --> pdb=" O PRO C 827 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE C 832 " --> pdb=" O MET C 828 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP C 833 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 846 No H-bonds generated for 'chain 'C' and resid 844 through 846' Processing helix chain 'C' and resid 860 through 865 removed outlier: 4.024A pdb=" N ASN C 864 " --> pdb=" O ASP C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 881 removed outlier: 3.880A pdb=" N THR C 872 " --> pdb=" O GLY C 868 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASN C 873 " --> pdb=" O GLY C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 893 removed outlier: 3.658A pdb=" N VAL C 890 " --> pdb=" O LYS C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 902 Processing helix chain 'C' and resid 908 through 925 removed outlier: 4.282A pdb=" N LYS C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 934 Processing helix chain 'C' and resid 941 through 950 removed outlier: 3.713A pdb=" N GLY C 950 " --> pdb=" O GLU C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 968 removed outlier: 4.386A pdb=" N ARG C 964 " --> pdb=" O PRO C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 987 through 998 removed outlier: 3.931A pdb=" N GLU C 991 " --> pdb=" O LEU C 987 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1013 Processing helix chain 'C' and resid 1013 through 1027 removed outlier: 3.704A pdb=" N ALA C1025 " --> pdb=" O LYS C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1040 Processing helix chain 'D' and resid 46 through 59 removed outlier: 3.510A pdb=" N LEU D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 124 through 134 removed outlier: 3.841A pdb=" N ALA D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 150 Processing helix chain 'D' and resid 151 through 162 removed outlier: 3.954A pdb=" N ALA D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 removed outlier: 3.596A pdb=" N TYR D 187 " --> pdb=" O PHE D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 228 removed outlier: 3.798A pdb=" N GLU D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 303 Processing helix chain 'D' and resid 332 through 340 removed outlier: 3.994A pdb=" N THR D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 339 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 354 Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 435 through 450 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 468 through 474 removed outlier: 3.538A pdb=" N LEU D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 481 removed outlier: 4.245A pdb=" N ILE D 481 " --> pdb=" O THR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 488 removed outlier: 3.647A pdb=" N PHE D 488 " --> pdb=" O PRO D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 510 removed outlier: 3.629A pdb=" N LEU D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 548 removed outlier: 3.773A pdb=" N LEU D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 571 through 578 removed outlier: 3.507A pdb=" N GLN D 575 " --> pdb=" O ARG D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.744A pdb=" N LEU D 587 " --> pdb=" O ARG D 583 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Proline residue: D 592 - end of helix Processing helix chain 'D' and resid 608 through 618 removed outlier: 3.522A pdb=" N PHE D 612 " --> pdb=" O GLY D 608 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP D 613 " --> pdb=" O GLY D 609 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET D 616 " --> pdb=" O PHE D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 655 through 670 removed outlier: 3.567A pdb=" N VAL D 659 " --> pdb=" O PRO D 655 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 670 " --> pdb=" O ALA D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 697 Processing helix chain 'D' and resid 719 through 734 Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'D' and resid 778 through 790 Processing helix chain 'D' and resid 798 through 802 Processing helix chain 'D' and resid 809 through 817 removed outlier: 3.723A pdb=" N LEU D 813 " --> pdb=" O SER D 809 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR D 817 " --> pdb=" O LEU D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 843 removed outlier: 3.885A pdb=" N VAL D 831 " --> pdb=" O PRO D 827 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 846 No H-bonds generated for 'chain 'D' and resid 844 through 846' Processing helix chain 'D' and resid 849 through 853 removed outlier: 3.756A pdb=" N ALA D 852 " --> pdb=" O ASP D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 870 Processing helix chain 'D' and resid 871 through 882 removed outlier: 3.791A pdb=" N ALA D 878 " --> pdb=" O LEU D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 removed outlier: 3.731A pdb=" N TYR D 894 " --> pdb=" O VAL D 890 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL D 895 " --> pdb=" O LYS D 891 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 925 Processing helix chain 'D' and resid 927 through 934 Processing helix chain 'D' and resid 941 through 950 Processing helix chain 'D' and resid 960 through 969 Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 988 through 998 Processing helix chain 'D' and resid 1003 through 1013 removed outlier: 3.904A pdb=" N VAL D1007 " --> pdb=" O THR D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1027 Processing helix chain 'D' and resid 1034 through 1040 Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.738A pdb=" N LEU A 564 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL A 796 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N MET A 566 " --> pdb=" O VAL A 796 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 604 through 605 removed outlier: 6.520A pdb=" N MET A 604 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N LEU A 642 " --> pdb=" O MET A 604 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET A 641 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 674 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 700 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N CYS A 739 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA A 702 " --> pdb=" O CYS A 739 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LYS A 741 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 704 " --> pdb=" O LYS A 741 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 738 " --> pdb=" O HIS A 769 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N HIS A 771 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 740 " --> pdb=" O HIS A 771 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1047 through 1050 removed outlier: 4.034A pdb=" N LEU A1058 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA A1062 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A1064 " --> pdb=" O PHE A1077 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.933A pdb=" N LEU B 564 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL B 796 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N MET B 566 " --> pdb=" O VAL B 796 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 604 through 605 removed outlier: 5.823A pdb=" N MET B 604 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU B 642 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE B 639 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ARG B 675 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET B 641 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE B 677 " --> pdb=" O MET B 641 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 643 " --> pdb=" O PHE B 677 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B 700 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N CYS B 739 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 702 " --> pdb=" O CYS B 739 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS B 741 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 738 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N HIS B 771 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE B 740 " --> pdb=" O HIS B 771 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1047 through 1051 removed outlier: 6.867A pdb=" N PHE B1077 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B1065 " --> pdb=" O GLN B1075 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN B1075 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 85 removed outlier: 6.486A pdb=" N VAL C 40 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE C 66 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL C 42 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS C 39 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N HIS C 115 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET C 41 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 206 through 207 removed outlier: 3.771A pdb=" N GLU C 236 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 325 through 326 removed outlier: 6.323A pdb=" N GLU C 246 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU C 262 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN C 248 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER C 266 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL C 275 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN C 268 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS C 273 " --> pdb=" O GLN C 268 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL C 274 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG C 377 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS C 372 " --> pdb=" O HIS C 432 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N HIS C 432 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 374 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE C 430 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS C 376 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS C 428 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL C 378 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 381 through 382 removed outlier: 3.702A pdb=" N GLN C 388 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.138A pdb=" N GLY C 392 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 396 through 398 removed outlier: 4.078A pdb=" N ARG C 451 " --> pdb=" O ARG C 398 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 564 through 566 removed outlier: 6.416A pdb=" N LEU C 564 " --> pdb=" O VAL C 794 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 768 " --> pdb=" O VAL C 793 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP C 795 " --> pdb=" O LEU C 768 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE C 770 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU C 738 " --> pdb=" O HIS C 769 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N HIS C 771 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE C 740 " --> pdb=" O HIS C 771 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL C 700 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N CYS C 739 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 702 " --> pdb=" O CYS C 739 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LYS C 741 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE C 704 " --> pdb=" O LYS C 741 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 701 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE C 639 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ARG C 675 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET C 641 " --> pdb=" O ARG C 675 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE C 677 " --> pdb=" O MET C 641 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU C 643 " --> pdb=" O PHE C 677 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET C 604 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N LEU C 642 " --> pdb=" O MET C 604 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ASN C 606 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 12.562A pdb=" N ARG C 644 " --> pdb=" O ASN C 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1048 through 1050 removed outlier: 3.531A pdb=" N PHE C1048 " --> pdb=" O ILE C1060 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C1060 " --> pdb=" O PHE C1048 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA C1062 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C1064 " --> pdb=" O PHE C1077 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1111 through 1112 removed outlier: 4.457A pdb=" N LEU C1175 " --> pdb=" O ILE C1112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1146 through 1150 removed outlier: 3.778A pdb=" N VAL C1149 " --> pdb=" O CYS C1138 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N CYS C1138 " --> pdb=" O VAL C1149 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C1122 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER C1141 " --> pdb=" O VAL C1120 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C1120 " --> pdb=" O SER C1141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 82 through 85 removed outlier: 6.340A pdb=" N VAL D 40 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE D 66 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL D 42 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 113 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 204 through 207 removed outlier: 3.509A pdb=" N ARG D 205 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 257 through 259 removed outlier: 3.842A pdb=" N GLU D 324 " --> pdb=" O GLU D 311 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 275 through 277 removed outlier: 3.657A pdb=" N VAL D 427 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 381 through 382 removed outlier: 3.802A pdb=" N GLN D 388 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 564 through 567 removed outlier: 8.587A pdb=" N GLU D 605 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP D 567 " --> pdb=" O GLU D 605 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TRP D 607 " --> pdb=" O ASP D 567 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ASN D 606 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 13.206A pdb=" N ARG D 644 " --> pdb=" O ASN D 606 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE D 639 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ARG D 675 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET D 641 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N PHE D 677 " --> pdb=" O MET D 641 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU D 643 " --> pdb=" O PHE D 677 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL D 700 " --> pdb=" O ILE D 737 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N CYS D 739 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA D 702 " --> pdb=" O CYS D 739 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS D 741 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE D 704 " --> pdb=" O LYS D 741 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU D 564 " --> pdb=" O VAL D 794 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL D 796 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N MET D 566 " --> pdb=" O VAL D 796 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1047 through 1051 removed outlier: 6.927A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL D1065 " --> pdb=" O GLN D1075 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN D1075 " --> pdb=" O VAL D1065 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1140 through 1141 removed outlier: 3.586A pdb=" N LEU D1140 " --> pdb=" O THR D1147 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR D1147 " --> pdb=" O LEU D1140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 1106 hydrogen bonds defined for protein. 3225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.42 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6340 1.33 - 1.45: 5556 1.45 - 1.57: 15588 1.57 - 1.70: 20 1.70 - 1.82: 264 Bond restraints: 27768 Sorted by residual: bond pdb=" N ILE C 516 " pdb=" CA ILE C 516 " ideal model delta sigma weight residual 1.458 1.493 -0.036 7.70e-03 1.69e+04 2.15e+01 bond pdb=" N ILE D 516 " pdb=" CA ILE D 516 " ideal model delta sigma weight residual 1.460 1.493 -0.034 7.50e-03 1.78e+04 2.05e+01 bond pdb=" N ILE D 86 " pdb=" CA ILE D 86 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.11e-02 8.12e+03 1.31e+01 bond pdb=" N VAL D 826 " pdb=" CA VAL D 826 " ideal model delta sigma weight residual 1.462 1.495 -0.034 1.01e-02 9.80e+03 1.10e+01 bond pdb=" N VAL C 164 " pdb=" CA VAL C 164 " ideal model delta sigma weight residual 1.461 1.501 -0.039 1.23e-02 6.61e+03 1.03e+01 ... (remaining 27763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 36966 2.50 - 4.99: 650 4.99 - 7.49: 53 7.49 - 9.98: 4 9.98 - 12.48: 4 Bond angle restraints: 37677 Sorted by residual: angle pdb=" C3B ACO C2001 " pdb=" O3B ACO C2001 " pdb=" P3B ACO C2001 " ideal model delta sigma weight residual 121.12 110.00 11.12 1.00e+00 1.00e+00 1.24e+02 angle pdb=" C3B ACO D2001 " pdb=" O3B ACO D2001 " pdb=" P3B ACO D2001 " ideal model delta sigma weight residual 121.12 110.04 11.08 1.00e+00 1.00e+00 1.23e+02 angle pdb=" PB ATP C2000 " pdb=" O3B ATP C2000 " pdb=" PG ATP C2000 " ideal model delta sigma weight residual 139.87 132.70 7.17 1.00e+00 1.00e+00 5.14e+01 angle pdb=" N VAL C 649 " pdb=" CA VAL C 649 " pdb=" C VAL C 649 " ideal model delta sigma weight residual 113.71 108.47 5.24 9.50e-01 1.11e+00 3.04e+01 angle pdb=" C ARG C 202 " pdb=" CA ARG C 202 " pdb=" CB ARG C 202 " ideal model delta sigma weight residual 116.63 110.97 5.66 1.16e+00 7.43e-01 2.38e+01 ... (remaining 37672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15067 17.95 - 35.89: 1302 35.89 - 53.84: 253 53.84 - 71.78: 74 71.78 - 89.72: 27 Dihedral angle restraints: 16723 sinusoidal: 6702 harmonic: 10021 Sorted by residual: dihedral pdb=" CB CYS B 752 " pdb=" SG CYS B 752 " pdb=" SG CYS B 786 " pdb=" CB CYS B 786 " ideal model delta sinusoidal sigma weight residual 93.00 179.39 -86.39 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS A 752 " pdb=" SG CYS A 752 " pdb=" SG CYS A 786 " pdb=" CB CYS A 786 " ideal model delta sinusoidal sigma weight residual 93.00 169.54 -76.54 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS D 752 " pdb=" SG CYS D 752 " pdb=" SG CYS D 786 " pdb=" CB CYS D 786 " ideal model delta sinusoidal sigma weight residual 93.00 141.06 -48.06 1 1.00e+01 1.00e-02 3.18e+01 ... (remaining 16720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3655 0.074 - 0.148: 478 0.148 - 0.221: 29 0.221 - 0.295: 1 0.295 - 0.369: 3 Chirality restraints: 4166 Sorted by residual: chirality pdb=" CB VAL C 164 " pdb=" CA VAL C 164 " pdb=" CG1 VAL C 164 " pdb=" CG2 VAL C 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA VAL C 164 " pdb=" N VAL C 164 " pdb=" C VAL C 164 " pdb=" CB VAL C 164 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ASN C 495 " pdb=" N ASN C 495 " pdb=" C ASN C 495 " pdb=" CB ASN C 495 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 4163 not shown) Planarity restraints: 4955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO D2001 " -0.099 2.00e-02 2.50e+03 8.17e-02 8.35e+01 pdb=" C5P ACO D2001 " 0.027 2.00e-02 2.50e+03 pdb=" C6P ACO D2001 " -0.074 2.00e-02 2.50e+03 pdb=" N4P ACO D2001 " 0.130 2.00e-02 2.50e+03 pdb=" O5P ACO D2001 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO C2001 " 0.099 2.00e-02 2.50e+03 8.16e-02 8.33e+01 pdb=" C5P ACO C2001 " -0.027 2.00e-02 2.50e+03 pdb=" C6P ACO C2001 " 0.074 2.00e-02 2.50e+03 pdb=" N4P ACO C2001 " -0.130 2.00e-02 2.50e+03 pdb=" O5P ACO C2001 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 199 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C GLY C 199 " 0.073 2.00e-02 2.50e+03 pdb=" O GLY C 199 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY C 200 " -0.024 2.00e-02 2.50e+03 ... (remaining 4952 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 1 1.81 - 2.58: 254 2.58 - 3.36: 35280 3.36 - 4.13: 63382 4.13 - 4.90: 113087 Nonbonded interactions: 212004 Sorted by model distance: nonbonded pdb=" CD2 LEU B1063 " pdb=" OE2 GLU B1079 " model vdw 1.040 3.460 nonbonded pdb=" CG LEU B1063 " pdb=" OE2 GLU B1079 " model vdw 1.859 3.470 nonbonded pdb=" O GLY C 199 " pdb=" O3A ATP C2000 " model vdw 1.948 3.040 nonbonded pdb=" OD1 ASP D 112 " pdb=" NH1 ARG D 137 " model vdw 1.956 3.120 nonbonded pdb=" O GLY C 199 " pdb=" O1A ATP C2000 " model vdw 1.989 3.040 ... (remaining 211999 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 33 through 1178) selection = (chain 'D' and resid 33 through 1178) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.010 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.416 27773 Z= 0.365 Angle : 0.745 12.475 37685 Z= 0.451 Chirality : 0.048 0.369 4166 Planarity : 0.005 0.082 4955 Dihedral : 14.488 89.725 10281 Min Nonbonded Distance : 1.040 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.54 % Favored : 93.40 % Rotamer: Outliers : 1.95 % Allowed : 1.08 % Favored : 96.97 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3485 helix: 1.05 (0.14), residues: 1419 sheet: -0.29 (0.23), residues: 501 loop : -1.63 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1070 TYR 0.023 0.001 TYR D 304 PHE 0.014 0.001 PHE C 920 TRP 0.016 0.002 TRP B 607 HIS 0.009 0.001 HIS B 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.27 (27768) covalent geometry : angle 0.74288 / 0.45 (37677) SS BOND : bond 0.00605 / 0.30 ( 4) SS BOND : angle 3.85671 / 2.86 ( 8) hydrogen bonds : bond 0.19418 / 13.28 ( 1106) hydrogen bonds : angle 7.00864 / 5.12 ( 3225) Misc. bond : bond 0.41585 / 21.89 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 376 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 828 MET cc_start: 0.8905 (mmm) cc_final: 0.8350 (mmm) REVERT: A 1022 ASP cc_start: 0.8510 (m-30) cc_final: 0.8277 (m-30) REVERT: B 566 MET cc_start: 0.8619 (ppp) cc_final: 0.8268 (ppp) REVERT: B 686 MET cc_start: 0.8958 (mpp) cc_final: 0.7907 (mpp) REVERT: B 923 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.9131 (pp30) REVERT: C 399 SER cc_start: 0.7462 (p) cc_final: 0.7144 (t) REVERT: C 663 CYS cc_start: 0.8510 (m) cc_final: 0.8301 (m) REVERT: C 724 MET cc_start: 0.8937 (mmp) cc_final: 0.8237 (mmm) REVERT: C 1054 ARG cc_start: 0.8425 (tmm-80) cc_final: 0.8220 (ttp80) REVERT: C 1116 MET cc_start: 0.0337 (tpt) cc_final: -0.0361 (mmt) REVERT: D 58 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7023 (tm-30) REVERT: D 139 ILE cc_start: 0.6372 (mt) cc_final: 0.5487 (mm) REVERT: D 401 GLU cc_start: 0.6891 (pm20) cc_final: 0.6557 (pm20) REVERT: D 430 ILE cc_start: 0.7248 (mt) cc_final: 0.6849 (mt) REVERT: D 881 MET cc_start: 0.8538 (mpp) cc_final: 0.8278 (mpp) REVERT: D 900 MET cc_start: 0.8479 (ptp) cc_final: 0.8218 (mtt) REVERT: D 967 VAL cc_start: 0.9055 (t) cc_final: 0.8841 (m) REVERT: D 1098 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7981 (tmm) outliers start: 56 outliers final: 4 residues processed: 408 average time/residue: 0.1705 time to fit residues: 108.0921 Evaluate side-chains 244 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 238 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 1020 PHE Chi-restraints excluded: chain D residue 1098 MET Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1073 GLN B 681 ASN ** B 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN B 923 GLN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 GLN C1040 GLN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN D 640 GLN D 653 ASN ** D 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1075 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.080844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.062885 restraints weight = 123677.258| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 5.96 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27773 Z= 0.198 Angle : 0.671 10.937 37685 Z= 0.344 Chirality : 0.045 0.254 4166 Planarity : 0.005 0.089 4955 Dihedral : 5.225 54.250 3827 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.89 % Favored : 93.08 % Rotamer: Outliers : 1.39 % Allowed : 9.30 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3485 helix: 0.96 (0.14), residues: 1459 sheet: -0.31 (0.22), residues: 526 loop : -1.65 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 288 TYR 0.022 0.002 TYR D 261 PHE 0.031 0.002 PHE C 387 TRP 0.015 0.002 TRP A 624 HIS 0.019 0.001 HIS B 879 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (27768) covalent geometry : angle 0.67012 / 0.34 (37677) SS BOND : bond 0.00597 / 0.30 ( 4) SS BOND : angle 2.24883 / 1.44 ( 8) hydrogen bonds : bond 0.04710 / 3.29 ( 1106) hydrogen bonds : angle 5.57346 / 4.09 ( 3225) Misc. bond : bond 0.00471 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 248 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 MET cc_start: 0.8716 (ppp) cc_final: 0.8375 (ppp) REVERT: B 671 MET cc_start: 0.8595 (tpp) cc_final: 0.8366 (tpp) REVERT: B 686 MET cc_start: 0.9006 (mpp) cc_final: 0.8211 (mpp) REVERT: B 690 MET cc_start: 0.9233 (mpp) cc_final: 0.8879 (mpp) REVERT: C 183 PHE cc_start: 0.8173 (m-80) cc_final: 0.7922 (m-80) REVERT: C 377 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7886 (ptt90) REVERT: C 395 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7300 (mt-10) REVERT: C 663 CYS cc_start: 0.8915 (m) cc_final: 0.8655 (m) REVERT: C 724 MET cc_start: 0.9113 (mmp) cc_final: 0.8312 (mmm) REVERT: C 828 MET cc_start: 0.8470 (ppp) cc_final: 0.8241 (ppp) REVERT: C 1054 ARG cc_start: 0.8892 (tmm-80) cc_final: 0.8473 (ttp80) REVERT: C 1067 ASP cc_start: 0.9308 (m-30) cc_final: 0.8847 (t70) REVERT: C 1086 SER cc_start: 0.7669 (p) cc_final: 0.7437 (p) REVERT: C 1116 MET cc_start: 0.0139 (tpt) cc_final: -0.0410 (tpp) REVERT: C 1143 MET cc_start: 0.5128 (ppp) cc_final: 0.4800 (ppp) REVERT: D 58 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7734 (tm-30) REVERT: D 139 ILE cc_start: 0.6439 (mt) cc_final: 0.5365 (mm) REVERT: D 459 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.7979 (mt) REVERT: D 471 PHE cc_start: 0.8201 (t80) cc_final: 0.7865 (t80) REVERT: D 820 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7668 (p) REVERT: D 967 VAL cc_start: 0.9159 (t) cc_final: 0.8929 (m) REVERT: D 1095 MET cc_start: 0.6966 (tmm) cc_final: 0.6752 (tmm) REVERT: D 1116 MET cc_start: 0.4185 (ttt) cc_final: 0.2910 (ptt) outliers start: 40 outliers final: 24 residues processed: 280 average time/residue: 0.1636 time to fit residues: 74.9543 Evaluate side-chains 244 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 187 TYR Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 1020 PHE Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 40 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 284 optimal weight: 50.0000 chunk 202 optimal weight: 6.9990 chunk 166 optimal weight: 0.2980 chunk 254 optimal weight: 10.0000 chunk 317 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 ASN A 769 HIS ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 864 ASN ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN D 350 HIS ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 HIS ** D 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.078756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.060835 restraints weight = 124979.719| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 6.01 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27773 Z= 0.213 Angle : 0.670 11.962 37685 Z= 0.341 Chirality : 0.044 0.261 4166 Planarity : 0.005 0.073 4955 Dihedral : 5.195 57.167 3821 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.49 % Favored : 92.48 % Rotamer: Outliers : 2.19 % Allowed : 11.81 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3485 helix: 0.86 (0.13), residues: 1486 sheet: -0.44 (0.23), residues: 516 loop : -1.69 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1036 TYR 0.022 0.002 TYR D 261 PHE 0.019 0.002 PHE A 876 TRP 0.013 0.002 TRP A 624 HIS 0.010 0.001 HIS D 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (27768) covalent geometry : angle 0.66935 / 0.34 (37677) SS BOND : bond 0.00523 / 0.26 ( 4) SS BOND : angle 1.88320 / 1.18 ( 8) hydrogen bonds : bond 0.04155 / 2.91 ( 1106) hydrogen bonds : angle 5.25993 / 3.89 ( 3225) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7227 (pp) REVERT: A 848 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8168 (p90) REVERT: B 566 MET cc_start: 0.8590 (ppp) cc_final: 0.8150 (ppp) REVERT: B 641 MET cc_start: 0.8893 (ppp) cc_final: 0.8676 (ppp) REVERT: B 686 MET cc_start: 0.9055 (mpp) cc_final: 0.8528 (mpp) REVERT: B 804 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8094 (tpp) REVERT: B 854 MET cc_start: 0.7835 (ppp) cc_final: 0.7477 (ppp) REVERT: C 48 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6538 (mp) REVERT: C 75 MET cc_start: 0.8083 (ptm) cc_final: 0.7762 (ptt) REVERT: C 149 MET cc_start: 0.8580 (mmm) cc_final: 0.7951 (mmt) REVERT: C 183 PHE cc_start: 0.8380 (m-80) cc_final: 0.7854 (m-80) REVERT: C 377 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8185 (ppt170) REVERT: C 395 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7417 (mt-10) REVERT: C 625 ARG cc_start: 0.9245 (mmm160) cc_final: 0.9040 (mmm-85) REVERT: C 663 CYS cc_start: 0.8961 (m) cc_final: 0.8697 (m) REVERT: C 724 MET cc_start: 0.9052 (mmp) cc_final: 0.8307 (mmm) REVERT: C 828 MET cc_start: 0.8438 (ppp) cc_final: 0.8219 (ppp) REVERT: C 1058 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8218 (pp) REVERT: C 1067 ASP cc_start: 0.9319 (m-30) cc_final: 0.9008 (t70) REVERT: C 1143 MET cc_start: 0.5343 (ppp) cc_final: 0.4891 (ppp) REVERT: D 44 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.6677 (m110) REVERT: D 75 MET cc_start: 0.8198 (tpt) cc_final: 0.7892 (tpt) REVERT: D 139 ILE cc_start: 0.6430 (mt) cc_final: 0.5439 (mm) REVERT: D 407 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7461 (tp) REVERT: D 423 ASP cc_start: 0.7744 (t0) cc_final: 0.7512 (t0) REVERT: D 471 PHE cc_start: 0.8260 (t80) cc_final: 0.7878 (t80) REVERT: D 820 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7865 (p) REVERT: D 848 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7309 (p90) REVERT: D 1116 MET cc_start: 0.4697 (ttt) cc_final: 0.3322 (ptt) REVERT: D 1145 MET cc_start: 0.6000 (ppp) cc_final: 0.5145 (mmp) outliers start: 63 outliers final: 31 residues processed: 269 average time/residue: 0.1558 time to fit residues: 68.0171 Evaluate side-chains 240 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 187 TYR Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1059 HIS Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 1020 PHE Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 215 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 333 optimal weight: 4.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN C1059 HIS D 436 HIS ** D 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.078538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.060652 restraints weight = 124717.786| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 5.92 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27773 Z= 0.180 Angle : 0.632 8.650 37685 Z= 0.319 Chirality : 0.043 0.175 4166 Planarity : 0.004 0.068 4955 Dihedral : 5.096 57.430 3821 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.92 % Favored : 93.06 % Rotamer: Outliers : 2.40 % Allowed : 13.69 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3485 helix: 0.93 (0.14), residues: 1489 sheet: -0.38 (0.23), residues: 518 loop : -1.66 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1070 TYR 0.019 0.001 TYR D 261 PHE 0.015 0.001 PHE D 920 TRP 0.014 0.002 TRP A 838 HIS 0.007 0.001 HIS B 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (27768) covalent geometry : angle 0.63101 / 0.32 (37677) SS BOND : bond 0.00481 / 0.24 ( 4) SS BOND : angle 1.93508 / 1.18 ( 8) hydrogen bonds : bond 0.03680 / 2.58 ( 1106) hydrogen bonds : angle 5.07761 / 3.75 ( 3225) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 220 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 TYR cc_start: 0.8140 (m-10) cc_final: 0.7923 (m-10) REVERT: A 822 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7240 (pp) REVERT: A 848 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8196 (p90) REVERT: B 566 MET cc_start: 0.8554 (ppp) cc_final: 0.8333 (ppp) REVERT: B 612 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: B 641 MET cc_start: 0.8978 (ppp) cc_final: 0.8645 (ppp) REVERT: B 686 MET cc_start: 0.9014 (mpp) cc_final: 0.8430 (mpp) REVERT: B 724 MET cc_start: 0.9029 (mpp) cc_final: 0.8797 (mpp) REVERT: B 804 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8049 (tpp) REVERT: B 854 MET cc_start: 0.7857 (ppp) cc_final: 0.7503 (ppp) REVERT: C 75 MET cc_start: 0.8108 (ptm) cc_final: 0.7840 (ptt) REVERT: C 395 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7439 (mt-10) REVERT: C 625 ARG cc_start: 0.9231 (mmm160) cc_final: 0.9009 (mmm-85) REVERT: C 663 CYS cc_start: 0.8975 (m) cc_final: 0.8720 (m) REVERT: C 724 MET cc_start: 0.9050 (mmp) cc_final: 0.8318 (mmm) REVERT: C 828 MET cc_start: 0.8420 (ppp) cc_final: 0.8162 (ppp) REVERT: C 854 MET cc_start: 0.7174 (mmm) cc_final: 0.6962 (mmt) REVERT: C 1058 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8242 (pp) REVERT: C 1067 ASP cc_start: 0.9302 (m-30) cc_final: 0.9004 (t0) REVERT: C 1143 MET cc_start: 0.5435 (ppp) cc_final: 0.4930 (ppp) REVERT: D 44 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.7147 (m-40) REVERT: D 75 MET cc_start: 0.8169 (tpt) cc_final: 0.7927 (tpt) REVERT: D 407 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7283 (tt) REVERT: D 423 ASP cc_start: 0.7785 (t0) cc_final: 0.7540 (t0) REVERT: D 471 PHE cc_start: 0.8405 (t80) cc_final: 0.8010 (t80) REVERT: D 820 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7884 (p) REVERT: D 848 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.7238 (p90) REVERT: D 886 LYS cc_start: 0.8719 (ptmm) cc_final: 0.8497 (tmtt) REVERT: D 896 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8486 (pm20) REVERT: D 1095 MET cc_start: 0.7446 (tmm) cc_final: 0.7196 (tmm) REVERT: D 1116 MET cc_start: 0.4791 (ttt) cc_final: 0.3217 (ptt) outliers start: 69 outliers final: 36 residues processed: 273 average time/residue: 0.1561 time to fit residues: 69.5292 Evaluate side-chains 252 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 187 TYR Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1059 HIS Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 896 GLU Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 20 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 280 optimal weight: 0.9990 chunk 332 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 304 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 HIS ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C 498 GLN ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.078265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.060341 restraints weight = 125078.461| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 5.85 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27773 Z= 0.174 Angle : 0.634 9.604 37685 Z= 0.319 Chirality : 0.043 0.220 4166 Planarity : 0.004 0.066 4955 Dihedral : 5.012 59.822 3819 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.75 % Allowed : 14.70 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3485 helix: 0.98 (0.14), residues: 1486 sheet: -0.42 (0.23), residues: 526 loop : -1.67 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1070 TYR 0.017 0.001 TYR D 261 PHE 0.015 0.001 PHE D 920 TRP 0.011 0.002 TRP C 838 HIS 0.012 0.001 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (27768) covalent geometry : angle 0.63368 / 0.32 (37677) SS BOND : bond 0.00666 / 0.34 ( 4) SS BOND : angle 2.01445 / 1.24 ( 8) hydrogen bonds : bond 0.03602 / 2.53 ( 1106) hydrogen bonds : angle 5.05379 / 3.74 ( 3225) Misc. bond : bond 0.00080 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 214 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 TYR cc_start: 0.8132 (m-10) cc_final: 0.7931 (m-10) REVERT: A 822 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7211 (pp) REVERT: A 848 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8218 (p90) REVERT: B 566 MET cc_start: 0.8509 (ppp) cc_final: 0.8282 (ppp) REVERT: B 612 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: B 641 MET cc_start: 0.8895 (ppp) cc_final: 0.8459 (ppp) REVERT: B 671 MET cc_start: 0.8636 (tpp) cc_final: 0.8159 (tpp) REVERT: B 686 MET cc_start: 0.9034 (mpp) cc_final: 0.8404 (mpp) REVERT: B 804 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8035 (tpp) REVERT: B 823 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: B 854 MET cc_start: 0.7999 (ppp) cc_final: 0.7600 (ppp) REVERT: C 48 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6534 (tp) REVERT: C 75 MET cc_start: 0.8136 (ptm) cc_final: 0.7885 (ptt) REVERT: C 149 MET cc_start: 0.8514 (mmp) cc_final: 0.7861 (mmt) REVERT: C 204 MET cc_start: 0.7506 (mtp) cc_final: 0.6619 (mmp) REVERT: C 395 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7456 (mt-10) REVERT: C 625 ARG cc_start: 0.9205 (mmm160) cc_final: 0.8509 (mmm-85) REVERT: C 628 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: C 663 CYS cc_start: 0.8968 (m) cc_final: 0.8720 (m) REVERT: C 724 MET cc_start: 0.9136 (mmp) cc_final: 0.8322 (mmm) REVERT: C 743 MET cc_start: 0.7522 (mmm) cc_final: 0.7220 (mmm) REVERT: C 828 MET cc_start: 0.8456 (ppp) cc_final: 0.8161 (ppp) REVERT: C 1058 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8260 (pp) REVERT: C 1067 ASP cc_start: 0.9262 (m-30) cc_final: 0.8940 (t0) REVERT: C 1143 MET cc_start: 0.5858 (ppp) cc_final: 0.5361 (ppp) REVERT: D 75 MET cc_start: 0.8205 (tpt) cc_final: 0.7979 (tpt) REVERT: D 423 ASP cc_start: 0.7721 (t0) cc_final: 0.7470 (t0) REVERT: D 471 PHE cc_start: 0.8495 (t80) cc_final: 0.8101 (t80) REVERT: D 848 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7419 (p90) REVERT: D 886 LYS cc_start: 0.8707 (ptmm) cc_final: 0.8474 (tmtt) REVERT: D 1116 MET cc_start: 0.5157 (ttt) cc_final: 0.3487 (ptt) REVERT: D 1145 MET cc_start: 0.5831 (ppp) cc_final: 0.4910 (mmt) outliers start: 79 outliers final: 48 residues processed: 278 average time/residue: 0.1589 time to fit residues: 71.5196 Evaluate side-chains 257 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 200 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 848 PHE Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1059 HIS Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 896 GLU Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 291 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 574 HIS ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 GLN C 414 GLN ** C 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1059 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 879 HIS D 956 HIS ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.077277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.059381 restraints weight = 125517.141| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 6.00 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27773 Z= 0.203 Angle : 0.661 14.679 37685 Z= 0.333 Chirality : 0.044 0.260 4166 Planarity : 0.005 0.065 4955 Dihedral : 4.975 54.161 3818 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.68 % Allowed : 15.74 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3485 helix: 0.87 (0.14), residues: 1494 sheet: -0.58 (0.23), residues: 532 loop : -1.68 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1070 TYR 0.017 0.002 TYR D 261 PHE 0.014 0.002 PHE D 920 TRP 0.015 0.002 TRP A 838 HIS 0.007 0.001 HIS B 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (27768) covalent geometry : angle 0.66072 / 0.33 (37677) SS BOND : bond 0.00439 / 0.22 ( 4) SS BOND : angle 1.81508 / 1.15 ( 8) hydrogen bonds : bond 0.03703 / 2.61 ( 1106) hydrogen bonds : angle 5.10692 / 3.79 ( 3225) Misc. bond : bond 0.00098 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 203 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7473 (pp) REVERT: A 848 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8187 (p90) REVERT: B 612 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: B 641 MET cc_start: 0.8901 (ppp) cc_final: 0.8507 (ppp) REVERT: B 686 MET cc_start: 0.9034 (mpp) cc_final: 0.8415 (mpp) REVERT: B 823 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7891 (m-30) REVERT: C 75 MET cc_start: 0.8119 (ptm) cc_final: 0.7891 (ptt) REVERT: C 149 MET cc_start: 0.8599 (mmp) cc_final: 0.8276 (mmt) REVERT: C 183 PHE cc_start: 0.8425 (m-80) cc_final: 0.8042 (m-80) REVERT: C 204 MET cc_start: 0.7800 (mtp) cc_final: 0.6850 (mmp) REVERT: C 395 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7411 (mt-10) REVERT: C 625 ARG cc_start: 0.9231 (mmm160) cc_final: 0.8874 (mmm-85) REVERT: C 663 CYS cc_start: 0.8969 (m) cc_final: 0.8731 (m) REVERT: C 686 MET cc_start: 0.9027 (mmt) cc_final: 0.8567 (mmt) REVERT: C 724 MET cc_start: 0.9095 (mmp) cc_final: 0.8329 (mmm) REVERT: C 828 MET cc_start: 0.8505 (ppp) cc_final: 0.8146 (ppp) REVERT: C 900 MET cc_start: 0.8805 (mmm) cc_final: 0.8326 (mmt) REVERT: C 1058 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8439 (pp) REVERT: C 1143 MET cc_start: 0.6221 (ppp) cc_final: 0.5705 (ppp) REVERT: D 75 MET cc_start: 0.8205 (tpt) cc_final: 0.7975 (tpt) REVERT: D 423 ASP cc_start: 0.7720 (t0) cc_final: 0.7466 (t0) REVERT: D 471 PHE cc_start: 0.8414 (t80) cc_final: 0.8134 (t80) REVERT: D 848 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7380 (p90) REVERT: D 896 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: D 1095 MET cc_start: 0.7234 (tmm) cc_final: 0.7012 (tmm) REVERT: D 1116 MET cc_start: 0.4983 (ttt) cc_final: 0.3452 (ptt) REVERT: D 1145 MET cc_start: 0.6006 (ppp) cc_final: 0.5183 (mmt) outliers start: 77 outliers final: 50 residues processed: 267 average time/residue: 0.1524 time to fit residues: 66.6189 Evaluate side-chains 251 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 194 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 848 PHE Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1059 HIS Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 896 GLU Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 78 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 281 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 232 optimal weight: 0.6980 chunk 333 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN B1073 GLN C 575 GLN ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1059 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.078968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.060972 restraints weight = 122679.415| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 6.12 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27773 Z= 0.117 Angle : 0.622 11.414 37685 Z= 0.306 Chirality : 0.043 0.290 4166 Planarity : 0.004 0.051 4955 Dihedral : 4.783 51.170 3818 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.02 % Allowed : 17.07 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3485 helix: 1.04 (0.14), residues: 1492 sheet: -0.43 (0.23), residues: 534 loop : -1.62 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1070 TYR 0.016 0.001 TYR D 261 PHE 0.014 0.001 PHE D 920 TRP 0.010 0.001 TRP A 838 HIS 0.009 0.001 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (27768) covalent geometry : angle 0.62116 / 0.31 (37677) SS BOND : bond 0.00384 / 0.19 ( 4) SS BOND : angle 1.79254 / 1.15 ( 8) hydrogen bonds : bond 0.03241 / 2.29 ( 1106) hydrogen bonds : angle 4.91065 / 3.63 ( 3225) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7470 (pp) REVERT: A 828 MET cc_start: 0.8905 (mmm) cc_final: 0.8642 (mmm) REVERT: A 848 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8170 (p90) REVERT: B 612 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7909 (m-80) REVERT: B 641 MET cc_start: 0.8825 (ppp) cc_final: 0.8388 (ppp) REVERT: B 686 MET cc_start: 0.9063 (mpp) cc_final: 0.8442 (mpp) REVERT: B 804 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8184 (tpp) REVERT: B 823 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: B 828 MET cc_start: 0.7665 (ptm) cc_final: 0.7431 (ptm) REVERT: B 864 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8451 (t0) REVERT: C 149 MET cc_start: 0.8680 (mmp) cc_final: 0.8476 (mmp) REVERT: C 204 MET cc_start: 0.7728 (mtp) cc_final: 0.6936 (mmp) REVERT: C 395 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7562 (mt-10) REVERT: C 403 MET cc_start: 0.8135 (mmm) cc_final: 0.7549 (tpp) REVERT: C 663 CYS cc_start: 0.8989 (m) cc_final: 0.8745 (m) REVERT: C 724 MET cc_start: 0.9185 (mmp) cc_final: 0.8305 (mmm) REVERT: C 743 MET cc_start: 0.7534 (mmm) cc_final: 0.7245 (mmm) REVERT: C 828 MET cc_start: 0.8489 (ppp) cc_final: 0.7973 (tmm) REVERT: C 1058 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8371 (pp) REVERT: C 1067 ASP cc_start: 0.9367 (m-30) cc_final: 0.8833 (t0) REVERT: C 1143 MET cc_start: 0.6237 (ppp) cc_final: 0.5702 (ppp) REVERT: D 75 MET cc_start: 0.8206 (tpt) cc_final: 0.7932 (tpt) REVERT: D 423 ASP cc_start: 0.7661 (t0) cc_final: 0.7398 (t0) REVERT: D 471 PHE cc_start: 0.8439 (t80) cc_final: 0.8172 (t80) REVERT: D 848 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7344 (p90) REVERT: D 896 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8360 (pm20) REVERT: D 1116 MET cc_start: 0.4821 (ttt) cc_final: 0.3207 (ptt) REVERT: D 1145 MET cc_start: 0.6002 (ppp) cc_final: 0.5180 (mmt) outliers start: 58 outliers final: 37 residues processed: 266 average time/residue: 0.1583 time to fit residues: 68.4613 Evaluate side-chains 249 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 848 PHE Chi-restraints excluded: chain B residue 864 ASN Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1073 GLN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 896 GLU Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 212 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 336 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 322 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 864 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS ** C 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 HIS ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.076672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.058726 restraints weight = 127150.327| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 6.17 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27773 Z= 0.230 Angle : 0.692 11.435 37685 Z= 0.349 Chirality : 0.045 0.295 4166 Planarity : 0.005 0.060 4955 Dihedral : 4.971 48.481 3818 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.51 % Allowed : 17.38 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3485 helix: 0.90 (0.14), residues: 1491 sheet: -0.58 (0.23), residues: 529 loop : -1.71 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1070 TYR 0.017 0.002 TYR B1013 PHE 0.017 0.002 PHE B1017 TRP 0.012 0.002 TRP C 838 HIS 0.010 0.001 HIS C 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.23 (27768) covalent geometry : angle 0.69147 / 0.35 (37677) SS BOND : bond 0.00359 / 0.18 ( 4) SS BOND : angle 2.01723 / 1.24 ( 8) hydrogen bonds : bond 0.03827 / 2.68 ( 1106) hydrogen bonds : angle 5.13350 / 3.80 ( 3225) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 202 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 MET cc_start: 0.8047 (ppp) cc_final: 0.7318 (ppp) REVERT: A 822 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7514 (pp) REVERT: A 848 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8177 (p90) REVERT: B 612 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: B 641 MET cc_start: 0.8823 (ppp) cc_final: 0.8328 (ppp) REVERT: B 686 MET cc_start: 0.9031 (mpp) cc_final: 0.8443 (mpp) REVERT: B 804 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8218 (tpp) REVERT: B 823 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: C 204 MET cc_start: 0.7792 (mtp) cc_final: 0.7252 (mtp) REVERT: C 395 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7551 (mt-10) REVERT: C 628 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: C 663 CYS cc_start: 0.8964 (m) cc_final: 0.8731 (m) REVERT: C 724 MET cc_start: 0.9120 (mmp) cc_final: 0.8362 (mmm) REVERT: C 828 MET cc_start: 0.8552 (ppp) cc_final: 0.8113 (tmm) REVERT: C 1058 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8232 (pp) REVERT: C 1096 LYS cc_start: 0.9361 (ptpp) cc_final: 0.9123 (ptpp) REVERT: C 1098 MET cc_start: 0.8516 (tpp) cc_final: 0.8196 (tpp) REVERT: C 1143 MET cc_start: 0.6288 (ppp) cc_final: 0.5657 (ppp) REVERT: D 75 MET cc_start: 0.8248 (tpt) cc_final: 0.8017 (tpt) REVERT: D 423 ASP cc_start: 0.7704 (t0) cc_final: 0.7465 (t0) REVERT: D 471 PHE cc_start: 0.8568 (t80) cc_final: 0.8280 (t80) REVERT: D 848 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.7471 (p90) REVERT: D 1116 MET cc_start: 0.4865 (ttt) cc_final: 0.3171 (ptt) REVERT: D 1145 MET cc_start: 0.5979 (ppp) cc_final: 0.5206 (mmt) outliers start: 72 outliers final: 42 residues processed: 262 average time/residue: 0.1543 time to fit residues: 66.5462 Evaluate side-chains 244 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 848 PHE Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 96 optimal weight: 0.6980 chunk 224 optimal weight: 5.9990 chunk 76 optimal weight: 0.0670 chunk 257 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 319 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 overall best weight: 1.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN B1073 GLN ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.078385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.060497 restraints weight = 123900.800| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 5.87 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27773 Z= 0.124 Angle : 0.658 10.918 37685 Z= 0.323 Chirality : 0.043 0.300 4166 Planarity : 0.004 0.052 4955 Dihedral : 4.851 48.561 3818 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.02 % Allowed : 18.04 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3485 helix: 1.01 (0.14), residues: 1493 sheet: -0.45 (0.23), residues: 531 loop : -1.63 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A1070 TYR 0.015 0.001 TYR C 118 PHE 0.016 0.001 PHE B 920 TRP 0.012 0.001 TRP A 838 HIS 0.007 0.001 HIS B 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (27768) covalent geometry : angle 0.65686 / 0.32 (37677) SS BOND : bond 0.00391 / 0.19 ( 4) SS BOND : angle 2.11809 / 1.27 ( 8) hydrogen bonds : bond 0.03330 / 2.35 ( 1106) hydrogen bonds : angle 4.94691 / 3.65 ( 3225) Misc. bond : bond 0.00087 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 209 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 MET cc_start: 0.8055 (ppp) cc_final: 0.7307 (ppp) REVERT: A 682 TYR cc_start: 0.7919 (t80) cc_final: 0.7618 (t80) REVERT: A 822 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7406 (pp) REVERT: A 848 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8187 (p90) REVERT: B 612 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: B 641 MET cc_start: 0.8777 (ppp) cc_final: 0.8244 (ppp) REVERT: B 686 MET cc_start: 0.9060 (mpp) cc_final: 0.8441 (mpp) REVERT: B 804 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8171 (tpp) REVERT: B 823 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: B 855 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8790 (mmtm) REVERT: C 149 MET cc_start: 0.8350 (mmp) cc_final: 0.7768 (mmt) REVERT: C 204 MET cc_start: 0.7755 (mtp) cc_final: 0.7265 (mtp) REVERT: C 395 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7541 (mt-10) REVERT: C 428 LYS cc_start: 0.6822 (tttt) cc_final: 0.6609 (tmtt) REVERT: C 628 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: C 663 CYS cc_start: 0.8958 (m) cc_final: 0.8703 (m) REVERT: C 724 MET cc_start: 0.9138 (mmp) cc_final: 0.8341 (mmm) REVERT: C 743 MET cc_start: 0.7500 (mmm) cc_final: 0.7234 (mmm) REVERT: C 828 MET cc_start: 0.8565 (ppp) cc_final: 0.8053 (tmm) REVERT: C 1058 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8204 (pp) REVERT: C 1116 MET cc_start: 0.0327 (OUTLIER) cc_final: 0.0116 (mmm) REVERT: C 1143 MET cc_start: 0.6227 (ppp) cc_final: 0.5700 (ppp) REVERT: C 1153 MET cc_start: 0.1048 (ppp) cc_final: 0.0824 (ppp) REVERT: D 423 ASP cc_start: 0.7687 (t0) cc_final: 0.7430 (t0) REVERT: D 471 PHE cc_start: 0.8472 (t80) cc_final: 0.8209 (t80) REVERT: D 783 MET cc_start: 0.9045 (tpp) cc_final: 0.8653 (mmt) REVERT: D 848 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7490 (p90) REVERT: D 870 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8586 (tt0) REVERT: D 1095 MET cc_start: 0.7332 (tmm) cc_final: 0.7098 (tmm) REVERT: D 1145 MET cc_start: 0.6025 (ppp) cc_final: 0.4707 (mmt) outliers start: 58 outliers final: 41 residues processed: 256 average time/residue: 0.1552 time to fit residues: 64.8132 Evaluate side-chains 253 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 848 PHE Chi-restraints excluded: chain B residue 855 LYS Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1073 GLN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1116 MET Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 870 GLN Chi-restraints excluded: chain D residue 886 LYS Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 232 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 320 optimal weight: 0.8980 chunk 333 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.078334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.060427 restraints weight = 124185.046| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 5.94 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27773 Z= 0.132 Angle : 0.668 12.200 37685 Z= 0.328 Chirality : 0.043 0.306 4166 Planarity : 0.004 0.057 4955 Dihedral : 4.819 48.067 3818 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.95 % Allowed : 18.18 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3485 helix: 1.09 (0.14), residues: 1481 sheet: -0.43 (0.23), residues: 531 loop : -1.60 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A1070 TYR 0.014 0.001 TYR D 261 PHE 0.014 0.001 PHE B 920 TRP 0.009 0.001 TRP C 838 HIS 0.006 0.001 HIS B 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (27768) covalent geometry : angle 0.66774 / 0.33 (37677) SS BOND : bond 0.00384 / 0.19 ( 4) SS BOND : angle 2.05719 / 1.26 ( 8) hydrogen bonds : bond 0.03323 / 2.34 ( 1106) hydrogen bonds : angle 4.91894 / 3.63 ( 3225) Misc. bond : bond 0.00051 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 MET cc_start: 0.8167 (ppp) cc_final: 0.7437 (ppp) REVERT: A 682 TYR cc_start: 0.7995 (t80) cc_final: 0.7751 (t80) REVERT: A 822 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7401 (pp) REVERT: A 848 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8172 (p90) REVERT: A 879 HIS cc_start: 0.7477 (m-70) cc_final: 0.7245 (m-70) REVERT: B 612 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: B 641 MET cc_start: 0.8717 (ppp) cc_final: 0.8172 (ppp) REVERT: B 686 MET cc_start: 0.9051 (mpp) cc_final: 0.8428 (mpp) REVERT: B 823 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: B 855 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8803 (mmtm) REVERT: C 149 MET cc_start: 0.8364 (mmp) cc_final: 0.7772 (mmt) REVERT: C 204 MET cc_start: 0.7762 (mtp) cc_final: 0.7257 (mtp) REVERT: C 276 GLU cc_start: 0.7806 (mp0) cc_final: 0.7583 (mp0) REVERT: C 395 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 428 LYS cc_start: 0.6686 (tttt) cc_final: 0.6467 (tmtt) REVERT: C 663 CYS cc_start: 0.8964 (m) cc_final: 0.8713 (m) REVERT: C 724 MET cc_start: 0.9159 (mmp) cc_final: 0.8364 (mmm) REVERT: C 743 MET cc_start: 0.7500 (mmm) cc_final: 0.7226 (mmm) REVERT: C 828 MET cc_start: 0.8534 (ppp) cc_final: 0.8032 (tmm) REVERT: C 900 MET cc_start: 0.8671 (mmm) cc_final: 0.8430 (mmm) REVERT: C 1058 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8232 (pp) REVERT: C 1116 MET cc_start: -0.0315 (OUTLIER) cc_final: -0.0534 (mmm) REVERT: C 1143 MET cc_start: 0.6308 (ppp) cc_final: 0.5772 (ppp) REVERT: D 423 ASP cc_start: 0.7645 (t0) cc_final: 0.7380 (t0) REVERT: D 471 PHE cc_start: 0.8485 (t80) cc_final: 0.8226 (t80) REVERT: D 848 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.7494 (p90) REVERT: D 870 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8562 (tt0) REVERT: D 1095 MET cc_start: 0.7409 (tmm) cc_final: 0.7181 (tmm) REVERT: D 1145 MET cc_start: 0.6075 (ppp) cc_final: 0.4962 (mmt) outliers start: 56 outliers final: 39 residues processed: 257 average time/residue: 0.1602 time to fit residues: 67.0832 Evaluate side-chains 254 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 848 PHE Chi-restraints excluded: chain B residue 855 LYS Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1116 MET Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 870 GLN Chi-restraints excluded: chain D residue 886 LYS Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 183 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 338 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 GLN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 GLN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.077108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.059136 restraints weight = 124310.948| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 6.06 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27773 Z= 0.190 Angle : 0.693 11.056 37685 Z= 0.343 Chirality : 0.044 0.313 4166 Planarity : 0.005 0.072 4955 Dihedral : 4.956 51.863 3818 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 1.99 % Allowed : 18.18 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3485 helix: 1.01 (0.14), residues: 1476 sheet: -0.55 (0.23), residues: 528 loop : -1.66 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1070 TYR 0.015 0.002 TYR B1013 PHE 0.017 0.001 PHE D 387 TRP 0.011 0.002 TRP C 838 HIS 0.008 0.001 HIS C 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (27768) covalent geometry : angle 0.69211 / 0.34 (37677) SS BOND : bond 0.00473 / 0.24 ( 4) SS BOND : angle 1.95618 / 1.20 ( 8) hydrogen bonds : bond 0.03612 / 2.53 ( 1106) hydrogen bonds : angle 5.02406 / 3.70 ( 3225) Misc. bond : bond 0.00054 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5423.14 seconds wall clock time: 94 minutes 2.35 seconds (5642.35 seconds total)